Publications

Outcome-guided Spike-and-Slab Lasso Biclustering: A Novel Approach for Enhancing Biclustering Techniques for Gene Expression Analysis

Published in Preprint, (arXiv, code), 2024

Biclustering has gained interest in gene expression data analysis due to its ability to identify groups of samples that exhibit similar behaviour in specific subsets of genes (or vice versa), in contrast to traditional clustering methods that classify samples based on all genes. Despite advances, biclustering remains a challenging problem, even with cutting-edge methodologies. This paper introduces an extension of the recently proposed Spike-and-Slab Lasso Biclustering (SSLB) algorithm, termed Outcome-Guided SSLB (OG-SSLB), aimed at enhancing the identification of biclusters in gene expression analysis. Our proposed approach integrates disease outcomes into the biclustering framework through Bayesian profile regression. By leveraging additional clinical information, OG-SSLB improves the interpretability and relevance of the resulting biclusters. Comprehensive simulations and numerical experiments demonstrate that OG-SSLB achieves superior performance, with improved accuracy in estimating the number of clusters and higher consensus scores compared to the original SSLB method. Furthermore, OG-SSLB effectively identifies meaningful patterns and associations between gene expression profiles and disease states. These promising results demonstrate the effectiveness of OG-SSLB in advancing biclustering techniques, providing a powerful tool for uncovering biologically relevant insights.

Recommended citation: Luis A. Vargas-Mieles, Paul D. W. Kirk and Chris Wallace, "Outcome-guided Spike-and-Slab Lasso Biclustering: A Novel Approach for Enhancing Biclustering Techniques for Gene Expression Analysis", arXiv preprint, arXiv:2412.08416. https://arxiv.org/abs/2412.08416

The split Gibbs sampler revisited: improvements to its algorithmic structure and augmented target distribution

Published in SIAM Journal on Imaging Sciences, (arXiv, code), 2023

This paper proposes a new accelerated proximal Markov chain Monte Carlo (MCMC) methodology to perform Bayesian computation efficiently in imaging inverse problems. The proposed methodology is derived from the Langevin diffusion process and stems from tightly integrating two state-of-the-art proximal Langevin MCMC samplers, SK-ROCK and split Gibbs sampling (SGS), which employ distinctively different strategies to improve convergence speed. More precisely, we show how to integrate, at the level of the Langevin diffusion process, the proximal SK-ROCK sampler which is based on a stochastic Runge-Kutta-Chebyshev approximation of the diffusion, with the model augmentation and relaxation strategy that SGS exploits to speed up Bayesian computation at the expense of asymptotic bias. This leads to a new and faster proximal SK-ROCK sampler that combines the accelerated quality of the original SK-ROCK sampler with the computational benefits of augmentation and relaxation. Moreover, rather than viewing the augmented and relaxed model as an approximation of the target model, positioning relaxation in a bias-variance trade-off, we propose to regard the augmented and relaxed model as a generalisation of the target model. This then allows us to carefully calibrate the amount of relaxation in order to simultaneously improve the accuracy of the model (as measured by the model evidence) and the sampler convergence speed. To achieve this, we derive an empirical Bayesian method to automatically estimate the optimal amount of relaxation by maximum marginal likelihood estimation. The proposed methodology is demonstrated with a range of numerical experiments related to image deblurring and inpainting, as well as with comparisons with alternative approaches from the state of the art.

Recommended citation: Marcelo Pereyra, Luis A. Vargas-Mieles, and Konstantinos C. Zygalakis, "The Split Gibbs Sampler Revisited: Improvements to Its Algorithmic Structure and Augmented Target Distribution", SIAM J. Imaging Sci., Vol. 16, No. 4, 2023, pp. 2040-2071. https://doi.org/10.1137/22M1506122

The forward–backward envelope for sampling with the overdamped Langevin algorithm

Published in Statistics and Computing, (arXiv), 2023

In this paper, we analyse a proximal method based on the idea of forward–backward splitting for sampling from distributions with densities that are not necessarily smooth. In particular, we study the non-asymptotic properties of the Euler–Maruyama discretization of the Langevin equation, where the forward–backward envelope is used to deal with the non-smooth part of the dynamics. An advantage of this envelope, when compared to widely-used Moreu–Yoshida one and the MYULA algorithm, is that it maintains the MAP estimator of the original non-smooth distribution. We also study a number of numerical experiments that support our theoretical findings.

Recommended citation: Armin Eftekhari, Luis A. Vargas-Mieles, and Konstantinos C. Zygalakis, "The forward–backward envelope for sampling with the overdamped Langevin algorithm", Statistics and Computing, Vol. 33, No. 85, 2023. https://link.springer.com/article/10.1007/s11222-023-10254-y

Accelerating Proximal Markov Chain Monte Carlo by Using an Explicit Stabilized Method

Published in SIAM Journal on Imaging Sciences, (arXiv, code), 2020

We present a highly efficient proximal Markov chain Monte Carlo methodology to perform Bayesian computation in imaging problems. Similarly to previous proximal Monte Carlo approaches, the proposed method is derived from an approximation of the Langevin diffusion. However, instead of the conventional Euler–Maruyama approximation that underpins existing proximal Monte Carlo methods, here we use a state-of-the-art orthogonal Runge–Kutta–Chebyshev stochastic approximation [A. Abdulle, I. Aimuslimani, and G. Vilmart, SIAM/ASA J. Uncertain. Quantif., 6 (2018), pp. 937–964] that combines several gradient evaluations to significantly accelerate its convergence speed, similarly to accelerated gradient optimization methods. The proposed methodology is demonstrated via a range of numerical experiments, including non-blind image deconvolution, hyperspectral unmixing, and tomographic reconstruction, with total-variation and $\ell_1$-type priors. Comparisons with Euler-type proximal Monte Carlo methods confirm that the Markov chains generated with our method exhibit significantly faster convergence speeds, achieve larger effective sample sizes, and produce lower mean-square estimation errors at equal computational budget.

Recommended citation: Marcelo Pereyra, Luis A. Vargas-Mieles, and Konstantinos C. Zygalakis, "Accelerating Proximal Markov Chain Monte Carlo by Using an Explicit Stabilized Method", SIAM J. Imaging Sci., Vol. 13, No. 2, 2020, pp. 87-118. https://doi.org/10.1137/19M1283719